PCNX1

protein-coding

pecanex 1

Gene summary

This gene encodes an evolutionarily conserved transmembrane protein similar to the pecanex protein in Drosophila. The fly protein is a component of the Notch signaling pathway, which functions in several developmental processes. [provided by RefSeq, Jul 2016]

Previous symbols:

PCNXL1
PCNX

MANE transcript

NM_014982.3

Inheritance

—

ClinVar variants

U:45B:18

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr14:70,907,405-71,115,382

External References & Databases

Ensembl (ENSG00000100731)

Transcript & Mutation Effects

hg38 • Region Span ~208.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCNX1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 23

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014982.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	6 clinvar	5 clinvar	14
missense			35 clinvar	3 clinvar	4 clinvar	42
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	45	9	9	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014982.3	RefSeq	NP_055797.2	36	MANE Select
ENST00000304743.7	Ensembl	ENSP00000304192.2	36	MANE Select
NM_001308160.2	RefSeq	NP_001295089.1	34	Standard
ENST00000439984.7	Ensembl	ENSP00000396617.3	34	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304743
Coding exons: 36
Length: 207978
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125748
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.43	1124	1.27e+3	0.887	0.0000687	15288
Missense (PolyPhen)		408	579.56	0.70398		6918
Synonymous	-0.375	474	464	1.02	0.0000236	4690
Loss of Function	8.35	17	113	0.151	0.00000674	1259

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00022	0.00016	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.105

Intolerance Scores

RVIS EVS: -1.95
RVIS percentile EVS: 1.87

Essentials

Essential (gene trap): N